In a mixing bowl, combine soy sauce, brown sugar, ketchup, pineapple juice, minced ginger, minced garlic, sesame oil, black pepper, and red pepper flakes (if using). Whisk until the sugar is dissolved and all ingredients are well mixed.
Place the chicken thighs in plastic wrap or foil and pour the marinade over them. Ensure the chicken is well coated. Marinate in the refrigerator for at least 30 minutes (up to overnight for more flavor).
Preheat your grill or grill pan over medium-high heat.
Remove the chicken from the marinade, allowing excess sauce to drip off. Reserve the marinade for basting.
Place the chicken on the grill over direct heat. Cook for about 7-10 minutes on each side, basting with the reserved marinade occasionally. Use a meat thermometer to check that the internal temperature reaches 165°F (75°C).
Once cooked, remove the chicken from the grill and let it rest for about 5 minutes before serving.
Garnish with sliced green onions and serve hot.